Mercurial > repos > peterjc > seq_filter_by_mapping
annotate tools/seq_filter_by_mapping/README.rst @ 2:48e71dfd51b3 draft
v0.0.5 Depend on Biopython 1.67 from Tool Shed or (Bio)conda
author | peterjc |
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date | Wed, 10 May 2017 13:16:44 -0400 |
parents | 8ff0ac66f1a3 |
children | 481b0a925e66 |
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0 | 1 Galaxy tool to filter FASTA, FASTQ or SFF sequences by SAM/BAM mapping |
2 ====================================================================== | |
3 | |
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4 This tool is copyright 2014-2017 by Peter Cock, The James Hutton Institute |
0 | 5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. |
6 See the licence text below. | |
7 | |
8 This tool is a short Python script (using Biopython library functions) which | |
9 divides a FASTA, FASTQ, or SFF file in two, those sequences which do or do | |
10 not map according to given SAM/BAM file(s). | |
11 | |
12 Example uses include mapping of FASTQ reads against a known contaminant | |
13 in order to remove reads prior to a de novo assembly. | |
14 | |
15 This tool is available from the Galaxy Tool Shed at: | |
16 | |
17 * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_mapping | |
18 | |
19 See also related tools: | |
20 | |
21 * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id | |
22 * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id | |
23 * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_rename | |
24 | |
25 | |
26 Automated Installation | |
27 ====================== | |
28 | |
29 This should be straightforward using the Galaxy Tool Shed, which should be | |
30 able to automatically install the dependency on Biopython and samtools | |
31 and then install this tool and run its unit tests. | |
32 | |
33 | |
34 Manual Installation | |
35 =================== | |
36 | |
37 There are just two files to install to use this tool from within Galaxy: | |
38 | |
39 * ``seq_filter_by_mapping.py`` (the Python script) | |
40 * ``seq_filter_by_mapping.xml`` (the Galaxy tool definition) | |
41 | |
42 The suggested location is a dedicated ``tools/seq_filter_by_mapping/`` folder. | |
43 | |
44 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the | |
45 tool. One suggested location is in the filters section. Simply add the line:: | |
46 | |
47 <tool file="seq_filter_by_mapping/seq_filter_by_mapping.xml" /> | |
48 | |
49 If you wish to run the unit tests, also move/copy the ``test-data/`` files | |
50 under Galaxy's ``test-data/`` folder. Then:: | |
51 | |
52 $ ./run_tests.sh -id seq_filter_by_mapping | |
53 | |
54 You will also need to install Biopython 1.54 or later. That's it. | |
55 | |
56 | |
57 History | |
58 ======= | |
59 | |
60 ======= ====================================================================== | |
61 Version Changes | |
62 ------- ---------------------------------------------------------------------- | |
63 v0.0.1 - Initial version. | |
64 v0.0.2 - Fixed some error messages. | |
1 | 65 v0.0.3 - Report counts for FASTQ as done for FASTA and SFF files. |
66 v0.0.4 - Use the ``format_source=...`` tag. | |
67 - Reorder XML elements (internal change only). | |
68 - Planemo for Tool Shed upload (``.shed.yml``, internal change only). | |
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69 v0.0.5 - Python script cleanups (internal change only). |
48e71dfd51b3
v0.0.5 Depend on Biopython 1.67 from Tool Shed or (Bio)conda
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70 - Depends on Biopython 1.67 via legacy Tool Shed package or bioconda. |
48e71dfd51b3
v0.0.5 Depend on Biopython 1.67 from Tool Shed or (Bio)conda
peterjc
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71 - Use ``<command detect_errors="aggressive">`` (internal change only). |
48e71dfd51b3
v0.0.5 Depend on Biopython 1.67 from Tool Shed or (Bio)conda
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72 - Single quote command line arguments (internal change only). |
0 | 73 ======= ====================================================================== |
74 | |
75 | |
76 Developers | |
77 ========== | |
78 | |
79 Development is on this GitHub repository: | |
80 https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping | |
81 | |
82 Much of the code was copied from my older tool: | |
83 https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id | |
84 | |
1 | 85 For pushing a release to the test or main "Galaxy Tool Shed", use the following |
86 Planemo commands (which requires you have set your Tool Shed access details in | |
87 ``~/.planemo.yml`` and that you have access rights on the Tool Shed):: | |
88 | |
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89 $ planemo shed_update -t testtoolshed --check_diff tools/seq_filter_by_mapping/ |
1 | 90 ... |
91 | |
92 or:: | |
0 | 93 |
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v0.0.5 Depend on Biopython 1.67 from Tool Shed or (Bio)conda
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94 $ planemo shed_update -t toolshed --check_diff tools/seq_filter_by_mapping/ |
1 | 95 ... |
96 | |
97 To just build and check the tar ball, use:: | |
0 | 98 |
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99 $ planemo shed_upload --tar_only tools/seq_filter_by_mapping/ |
1 | 100 ... |
101 $ tar -tzf shed_upload.tar.gz | |
102 test-data/SRR639755_mito_pairs.fastq.gz | |
103 test-data/SRR639755_sample_by_coord.sam | |
104 test-data/SRR639755_sample_lax.fastq | |
105 test-data/SRR639755_sample_strict.fastq | |
0 | 106 tools/seq_filter_by_mapping/README.rst |
107 tools/seq_filter_by_mapping/seq_filter_by_mapping.py | |
108 tools/seq_filter_by_mapping/seq_filter_by_mapping.xml | |
109 tools/seq_filter_by_mapping/tool_dependencies.xml | |
110 | |
111 | |
112 Licence (MIT) | |
113 ============= | |
114 | |
115 Permission is hereby granted, free of charge, to any person obtaining a copy | |
116 of this software and associated documentation files (the "Software"), to deal | |
117 in the Software without restriction, including without limitation the rights | |
118 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | |
119 copies of the Software, and to permit persons to whom the Software is | |
120 furnished to do so, subject to the following conditions: | |
121 | |
122 The above copyright notice and this permission notice shall be included in | |
123 all copies or substantial portions of the Software. | |
124 | |
125 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | |
126 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | |
127 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | |
128 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | |
129 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | |
130 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | |
131 THE SOFTWARE. |